Confirmed the problem is with Mod Organizer, somehow, I can run the FNV Launcher, NVSE, and FNV4GB normally and it works every time. The moment I try to load any of them through Mod Organizer, I get black screen and freeze on startup.
As for my Mod Order... there is none. I'm only on the Extender section of F&LiNV. The only plugins are the DLC.
EDIT: Neverind, I'm an idiot. Like an earlier poster, I didn't have all my BSAs checked on the Archive tab. *SIGH*
Barachiel's post in Can't Start New Vegas Through MO was marked as the answer